Mercurial > repos > iuc > hyphy_conv

annotate test-data/gard-out1.json @ 1:c1d24ff838c8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
author iuc
date Tue, 20 Apr 2021 19:55:16 +0000
parents 9ce3d6d4bd0e
children f6e7b5955712
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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1 {
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2 "analysis":{
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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3 "authors":"Sergei L Kosakovsky Pond",
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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4 "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901",
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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5 "contact":"spond@temple.edu",
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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6 "info":"GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic\n approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic\n incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the\n placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc\n tests run to distinguish topological incongruence from rate-variation.",
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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7 "requirements":"A sequence alignment.",
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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8 "version":"0.1"
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9 },
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10 "baselineScore":8884.998566352424,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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11 "breakpointData":{
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12 "0":{
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17 },
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35 }
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36 },
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37 "improvements":{
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39 "breakpoints": [
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41 ],
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42 "deltaAICc":121.2176698921212
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57 "deltaAICc":0.1679528998429305
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58 }
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60 "input":{
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iuc
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diff changeset
61 "file name":"/Users/ryanvelazquez/Documents/galaxy_items/tools-iuc/tools/hyphy/./test-data/gard-in1.fa",
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
62 "number of sequences":21,
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iuc
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diff changeset
63 "number of sites":1698,
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iuc
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diff changeset
64 "partition count":1
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iuc
parents:
diff changeset
65 },
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iuc
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diff changeset
66 "potentialBreakpoints":244,
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iuc
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diff changeset
67 "singleTreeAICc":8952.770360670584,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
68 "siteBreakPointSupport":{
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iuc
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diff changeset
69 "1005":3.828454313051127e-38,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
70 "1006":3.079286891225441e-38,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
71 "101":1.367441431357884e-42,
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iuc
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diff changeset
72 "1013":1.999228647805731e-38,
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iuc
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diff changeset
73 "1015":5.581552407151915e-37,
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iuc
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diff changeset
74 "1016":6.637544467285419e-30,
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iuc
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diff changeset
75 "1020":8.283127276807708e-36,
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iuc
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diff changeset
76 "1021":5.149224738126319e-36,
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iuc
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diff changeset
77 "1023":2.572721275288951e-33,
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iuc
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diff changeset
78 "1031":1.729227457250037e-39,
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iuc
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diff changeset
79 "1041":4.668316272061274e-41,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
80 "1052":7.068163653642667e-45,
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iuc
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diff changeset
81 "1058":4.410408926058965e-40,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
82 "1061":3.620416399436108e-31,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
83 "1070":1.30023862441172e-32,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
84 "1073":2.392244771912456e-29,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
85 "108":1.088323481504585e-09,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
86 "1082":1.781042369034824e-32,
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iuc
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diff changeset
87 "1085":1.072215721126058e-30,
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iuc
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diff changeset
88 "1106":8.711808244586844e-32,
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iuc
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diff changeset
89 "1124":2.066632617058007e-32,
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iuc
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diff changeset
90 "1130":2.365201133574919e-32,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
91 "1136":1.180024224431614e-32,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
92 "1149":2.0594328664778e-30,
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iuc
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diff changeset
93 "116":3.062613098803733e-06,
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iuc
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diff changeset
94 "1166":1.382998480016903e-28,
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iuc
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diff changeset
95 "1206":4.271112529885021e-30,
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iuc
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diff changeset
96 "1223":2.439400027544238e-30,
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iuc
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diff changeset
97 "1250":2.1846050762587e-31,
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iuc
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diff changeset
98 "1271":1.963370249731928e-32,
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iuc
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diff changeset
99 "1286":1.143587697307953e-32,
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iuc
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diff changeset
100 "1292":1.940620880105886e-32,
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iuc
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diff changeset
101 "1298":1.19984441620646e-32,
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iuc
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diff changeset
102 "1319":5.201055420999954e-33,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
103 "1322":1.490898155414118e-32,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
104 "1334":6.386384600277327e-33,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
105 "134":7.744769428033727e-17,
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iuc
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diff changeset
106 "1361":2.822486839844269e-33,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
107 "1384":1.557822413676087e-33,
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iuc
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diff changeset
108 "1397":1.068642031138833e-35,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
109 "1412":6.831611952947673e-38,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
110 "1418":1.522690852126543e-39,
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iuc
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diff changeset
111 "1430":7.96352395927298e-40,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
112 "1433":1.156793517215151e-37,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
113 "1436":5.651778976453802e-38,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
114 "144":8.552230281908163e-07,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
115 "1442":2.016530452321108e-37,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
116 "1454":2.386567702095966e-36,
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iuc
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diff changeset
117 "1463":9.043007916183422e-39,
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iuc
parents:
diff changeset
118 "1465":7.669880260535686e-39,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
119 "1473":3.675784601460829e-36,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
120 "1481":2.661546849207671e-37,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
121 "149":1.304259029589306e-05,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
122 "1495":4.622941797307467e-44,
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iuc
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diff changeset
123 "1496":4.226996151791482e-44,
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iuc
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diff changeset
124 "1499":2.730615034063184e-44,
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iuc
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diff changeset
125 "151":1.790975065283929e-08,
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iuc
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diff changeset
126 "1515":4.749012537570416e-45,
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iuc
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diff changeset
127 "1516":1.058313486583168e-45,
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iuc
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diff changeset
128 "1519":3.729412022561233e-46,
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iuc
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diff changeset
129 "1520":2.407045351616036e-46,
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iuc
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130 "1521":1.689577693820857e-46,
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iuc
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131 "1523":5.07686612591507e-46,
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iuc
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132 "1524":1.741238756038766e-46,
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iuc
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diff changeset
133 "1526":3.855324589536673e-46,
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iuc
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diff changeset
134 "1537":2.062102436942228e-46,
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iuc
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diff changeset
135 "1538":3.417841619348906e-47,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
136 "1539":3.047730711305713e-47,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
137 "1544":1.7639941893744e-47,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
138 "155":1.315748190900565e-29,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
139 "1556":1.89572005098281e-47,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
140 "1580":5.505818788734445e-49,
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
diff changeset
141 "1585":1.614020745294316e-49,
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diff changeset
142 "159":2.814745521856487e-30,
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iuc
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143 "161":5.278607654454491e-08,
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iuc
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144 "1610":6.983674612335563e-50,
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iuc
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145 "1613":1.219959907173526e-49,
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iuc
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146 "1616":1.379005387331829e-49,
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iuc
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147 "1618":1.403866743396411e-51,
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iuc
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148 "1619":6.05913881499244e-52,
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149 "1631":1.563107434100785e-52,
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iuc
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150 "1632":5.045949522041951e-52,
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151 "1644":1.457045566204417e-52,
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iuc
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152 "1646":1.817307863422175e-52,
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153 "1658":2.336582715408929e-53,
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154 "173":3.057688318766887e-09,
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185 "328":5.468914334726157e-06,
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190 "383":1.208370214471027e-18,
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192 "407":6.023041146737167e-09,
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193 "414":5.844791249373782e-06,
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194 "417":1.35252270798266e-09,
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197 "424":1.929854665115397e-05,
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199 "426":4.822853182787663e-05,
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201 "437":3.538850116792625e-27,
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204 "45":5.811735655101648e-16,
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209 "461":1,
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212 "467":1.657561796358788e-05,
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214 "498":1.148320825350936e-24,
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215 "50":8.32428744865e-23,
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216 "509":1.189408841111924e-08,
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217 "511":2.022119078897978e-24,
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218 "513":3.201599896136264e-07,
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219 "518":2.988923843741992e-13,
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220 "522":2.646016563727863e-07,
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221 "524":2.999275395428511e-07,
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222 "531":7.048583824652365e-06,
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iuc
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274 "812":2.065239894547715e-33,
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276 "833":1.55354314155857e-30,
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279 "845":2.516382791081784e-31,
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282 "872":1.784676508419814e-43,
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283 "878":2.0081213960433e-43,
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284 "887":1.13493422288884e-43,
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285 "891":1.700300743179312e-36,
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286 "905":1.109981525417329e-42,
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287 "911":2.50641030292061e-44,
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288 "917":1.208124588626152e-44,
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289 "926":5.840308910078806e-45,
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290 "932":2.793211015138247e-45,
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295 "978":2.723057526622017e-45,
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296 "98":2.547710617920883e-27,
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299 "992":1.349612353859241e-47,
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300 "995":3.874956487042822e-49
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iuc
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diff changeset
301 },
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iuc
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diff changeset
302 "timeElapsed":1045,
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iuc
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diff changeset
303 "totalModelCount":4369,
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iuc
parents:
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304 "trees":{
9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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diff changeset
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9ce3d6d4bd0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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